OpenScience / Software



RnaViz

Posted on February 28, 2001 by Dan Gezelter

RnaViz is a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files. The layout of a structure … Continue reading →

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Posted in Biochemistry | Leave a comment

SCORE

Posted on February 28, 2001 by Dan Gezelter

SCORE is an empirical method developed for estimating the binding affinity of protein-ligand complex with known three-dimensional structure. Find SCORE at: http://mdl.ipc.pku.edu.cn/drug_design/work/score.html

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Posted in Biochemistry | Leave a comment

SeqPup

Posted on February 28, 2001 by Dan Gezelter

SeqPup is a biological sequence editor and analysis program. Find SeqPup at: http://iubio.bio.indiana.edu/IUBio-Software+Data/molbio/seqpup/java/

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Posted in Bioinformatics | Leave a comment

NanoCAD

Posted on February 28, 2001 by Dan Gezelter

A freeware nanotech design system in Java Find NanoCAD at: http://server.ccl.net/cca/software/SOURCES/JAVA/ncad/unpacked/ncad.html

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Posted in Nanotechnology | Leave a comment

Populations

Posted on February 28, 2001 by Dan Gezelter

Population genetic software (individuals or populations distances, phylogenetic trees) Find Populations at: http://bioinformatics.org/~tryphon/populations/

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GDPC

Posted on February 27, 2001 by Dan Gezelter

gdpc is a program for visualising molecular dynamic simulations Find GDPC at: http://www.frantz.fi/software/gdpc.php

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Posted in Molecular Dynamics | Leave a comment

Geanfammer

Posted on February 27, 2001 by Dan Gezelter

geanfammer contains divclus which divides proteinclusters into more correct domain level clusters Find Geanfammer at: http://www.mrc-lmb.cam.ac.uk/genomes/geanfammer.html

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gOpenMol

Posted on February 27, 2001 by Dan Gezelter

gOpenMol is the graphical interface into the OpenMol set of computational chemistry programs Find gOpenMol at: http://www.csc.fi/english/pages/g0penMol

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Posted in Molecule Viewers and Editors | Leave a comment

HMMER

Posted on February 27, 2001 by Dan Gezelter

Profile hidden Markov models for biological sequence analysis. Find HMMER at: http://hmmer.janelia.org/

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Pfam

Posted on February 27, 2001 by Dan Gezelter

Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains. Find Pfam at: http://pfam.sanger.ac.uk/

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Posted in Bioinformatics | Leave a comment